Environmental pollution is one of the major problems of these days. One of the reasons of environmental pollution is the indiscriminate use of agrochemicals in agriculture. Fungicides are being extensively used in agriculture for enhancing crop yield and growth by controlling fungal growth. Fungicide carbendazim is widely applied to soil and seeds of vegetable/cereal crops in India and is effective against a very broad spectrum of fungi. The present study was designed to monitor the cyto-genotoxic effects of carbendazim directly in treated soils by cytogenetical analysis using Allium cepa root tip bioassay. In a pot experiment, fungicide carbendazim was added to soil at the rates of 2.5, 5, 7.5, and 10 mg kg−1 soil and uniform size onion bulb was planted in each pot, and three replicates were maintained for each dose at 1, 7, 15, 30, and 45 days after application and roots from onion bulbs were fixed for cytogenetical analysis. Findings indicate that carbendazim treatment leads to a significant dose and duration-dependent decrease in percent mitotic index with related increase in mitotic inhibition. Statistical analysis showed a significant effect of carbendazim doses and duration of treatment on the percentage relative abnormality rate of A. cepa. Phase indices of our study showed high numbers of cells in prophase as compared to other phases at some doses of treatment. The different types of chromosomal abnormalities observed in our study serve as indicators of genotoxicity of carbendazim and we report for the first time the effect of its application directly in soil using a plant test system.